I have a model with quant vars only and the error message does not make sense:
(mod1 <- coxph(Surv(time=strt,time2=stp,event=(resp==1))~
+incpost+I(amt/1e5)+rate+strata(termfac),
subset=dt<"2010-08-30", data=inc,method="efron"))
Call:
coxph(formula = Surv(time = strt, time2 = stp, event = (resp ==
1)) ~ +incpost + I(amt/1e+05) + rate + strata(termfac), data = inc,
subset = dt < "2010-08-30", method = "efron")
coef exp(coef) se(coef) z p
incpost 0.2563 1.292 0.02479 10.34 0.0e+00
I(amt/1e+05) -0.0532 0.948 0.00487 -10.92 0.0e+00
rate -0.0507 0.951 0.00945 -5.36 8.2e-08
Likelihood ratio test=295 on 3 df, p=0 n= 1192634
> length(mod1$xlevels)
[1] 0
# now calling survfit with just a few rows from the data
> s1 <- survfit(mod1,newdata=inc[50050:50100,],se.fit=F,individual=T,type="aa")
Error in `contrasts<-`(`*tmp*`, value = "contr.treatment") :
contrasts can be applied only to factors with 2 or more levels
> inc[50050:50100,]
dt inc incpost strt stp resp rate amt p1 matfac termfac
vol
50050 2009-02-05 0.00000 0.00 0 1 0 5.35 266833 C 5 3
14229571
50051 2009-02-06 -0.09575 0.00 1 2 0 5.35 266833 C 5 3
14229571
50052 2009-02-09 -0.03875 0.00 4 5 0 5.35 266833 C 5 3
14229571
50053 2009-02-10 0.00850 0.00 5 6 0 5.35 266833 C 5 3
14229571
50054 2009-02-11 0.00250 0.00 6 7 0 5.35 266833 C 5 3
14229571
50055 2009-02-12 -0.04725 0.00 7 8 0 5.35 266833 C 5 3
14229571
50056 2009-02-13 -0.00075 0.00 8 9 0 5.35 266833 C 5 3
14229571
50057 2009-02-16 -0.10425 0.00 11 12 0 5.35 266833 C 5 3
14229571
50058 2009-02-17 -0.10425 0.00 12 13 0 5.35 266833 C 5 3
14229571
50059 2009-02-18 -0.02925 0.00 13 14 0 5.35 266833 C 5 3
14229571
50060 2009-02-19 -0.01300 0.00 14 15 0 5.35 266833 C 5 3
14229571
50061 2009-02-20 -0.04075 0.00 15 16 0 5.35 266833 C 5 3
14229571
50062 2009-02-23 -0.03100 0.00 18 19 0 5.35 266833 C 5 3
14229571
50063 2009-02-24 0.01975 0.00 19 20 0 5.35 266833 C 5 3
14229571
50064 2009-02-25 0.13050 0.00 20 21 0 5.35 266833 C 5 3
14229571
50065 2009-02-26 0.12725 0.00 21 22 0 5.35 266833 C 5 3
14229571
... further output truncated
Please, comment if you see what's the issue.
Thank you.
Stephen
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